Contacts of the helix formed by residues 8 - 34 (chain O) in PDB entry 2BKC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 8 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O VAL* 1.3 76.7 - - - +
9O THR* 1.3 65.1 + - - +
10O LYS* 3.6 19.3 + - - +
11O GLU* 3.3 29.9 + - - +
12O PHE* 3.0 21.8 + - - +
119O LEU* 3.8 3.9 - - - +
123O GLU* 3.3 21.5 - - - +
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Residues in contact with THR 9 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8O ASP* 1.3 74.8 - - - +
10O LYS* 1.3 64.7 + - - +
12O PHE* 3.1 7.0 + - + +
13O LEU* 3.0 43.3 + - + +
67O ILE* 4.1 7.9 - - + -
119O LEU* 4.1 8.8 - - - +
120O THR* 3.7 14.4 + - - +
123O GLU* 3.1 28.5 + - - +
125O ASP* 3.6 24.9 - - - +
128O THR* 4.0 11.2 - - + -
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Residues in contact with LYS 10 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8O ASP* 3.3 16.9 + - - +
9O THR* 1.3 78.9 - - - +
11O GLU* 1.3 57.7 + - - +
14O ASN* 3.2 28.8 + - - +
64O LEU* 3.5 20.6 - - + +
67O ILE* 2.8 45.7 + - + -
68O GLY* 3.5 14.3 + - - +
69O GLY* 4.1 13.2 - - - -
155T LEU* 5.5 2.2 - - - +
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Residues in contact with GLU 11 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O VAL* 3.5 35.0 - - + +
8O ASP* 3.3 23.1 + - - +
10O LYS* 1.3 76.8 - - - +
12O PHE* 1.3 66.4 + - - +
14O ASN* 4.1 3.9 - - - +
15O HIS* 3.0 26.0 + - - +
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Residues in contact with PHE 12 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O VAL* 5.2 3.3 - - + +
8O ASP 3.0 12.9 + - - +
9O THR* 3.1 9.4 + - + +
11O GLU* 1.3 78.2 - - - +
13O LEU* 1.3 74.3 + - + +
15O HIS* 3.3 7.4 + - - +
16O GLN* 3.1 57.4 + - + +
112O GLU* 2.9 35.7 - - + -
113O TYR* 3.9 6.1 - + - -
115O GLN* 4.6 7.9 - - + -
116O GLY* 3.6 28.9 - - - -
119O LEU* 3.9 17.0 - - + -
128O THR* 6.1 0.2 - - + -
132O LEU* 4.1 22.7 - - + -
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Residues in contact with LEU 13 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9O THR* 3.0 25.5 + - + +
10O LYS 4.0 2.9 - - - +
12O PHE* 1.3 90.4 - - + +
14O ASN* 1.3 62.0 + - - +
16O GLN* 3.1 4.0 + - + +
17O VAL* 3.0 24.0 + - - +
60O VAL* 3.2 32.2 - - + +
63O ARG* 4.5 4.7 - - + -
64O LEU* 4.3 21.1 - - + +
67O ILE* 4.3 13.5 - - + -
128O THR* 3.7 37.9 - - + +
131O MET* 3.9 14.8 - - + -
132O LEU* 4.2 8.1 - - + -
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Residues in contact with ASN 14 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10O LYS 3.2 16.9 + - - +
11O GLU* 4.1 4.0 - - - +
13O LEU* 1.3 77.0 - - - +
15O HIS* 1.3 65.7 + - - +
17O VAL* 3.2 8.3 + - - +
18O ALA 3.1 17.3 + - - -
64O LEU* 3.5 14.4 - - + +
70O SER 2.9 27.1 + - - +
71O PRO* 3.4 4.7 - - - +
72O PHE* 2.9 58.8 + - + +
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Residues in contact with HIS 15 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O GLU 3.0 19.0 + - - +
12O PHE* 3.3 8.2 - - - +
14O ASN* 1.3 77.1 - - - +
16O GLN* 1.3 73.8 + - - +
18O ALA* 3.3 8.0 + - - +
19O ASN* 3.0 31.1 + - - +
72O PHE* 4.4 5.1 - - - -
81O ASN* 2.9 33.8 + - + -
83O SER* 3.3 24.2 + - - -
112O GLU* 3.1 22.6 + - - -
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Residues in contact with GLN 16 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O PHE* 3.1 46.7 + - + +
13O LEU* 3.1 10.3 + - + +
15O HIS* 1.3 92.0 + - - +
17O VAL* 1.3 58.7 + - - +
19O ASN* 3.0 18.3 + - - +
20O LEU* 2.9 40.6 + - + +
60O VAL* 4.3 10.8 - - + -
109O LEU* 3.7 8.1 - - - +
112O GLU* 2.9 26.9 + - - +
113O TYR* 3.3 30.3 - - + -
132O LEU* 5.8 1.1 - - + -
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Residues in contact with VAL 17 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M TRP* 4.3 13.7 - - + -
13O LEU 3.0 19.1 + - - +
14O ASN* 3.2 21.5 + - - +
16O GLN* 1.3 75.5 - - - +
18O ALA* 1.3 59.4 + - - +
21O ASN* 2.6 45.1 + - - +
57O MET* 4.2 9.8 - - - +
60O VAL* 3.6 17.0 - - + +
61O ALA* 4.0 20.4 - - + +
64O LEU* 4.9 1.6 - - + -
71O PRO* 4.7 3.1 - - + -
72O PHE* 3.6 24.5 - - + +
78O PHE* 4.0 3.8 - - + -
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Residues in contact with ALA 18 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O ASN 3.1 10.7 + - - +
15O HIS 3.5 7.9 - - - +
16O GLN 3.2 0.2 - - - -
17O VAL* 1.3 75.6 - - - +
19O ASN* 1.3 63.1 + - - +
20O LEU 3.3 0.2 + - - -
21O ASN* 3.3 3.6 + - - +
22O VAL* 3.2 24.9 + - - +
72O PHE* 4.3 2.7 - - + -
78O PHE* 3.5 41.5 - - + +
81O ASN* 4.0 11.9 - - + -
82O ALA* 3.9 12.8 - - - +
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Residues in contact with ASN 19 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15O HIS* 3.0 17.7 + - - +
16O GLN* 3.0 34.9 + - - +
18O ALA* 1.3 71.4 - - - +
20O LEU* 1.3 58.3 + - - +
22O VAL* 3.4 3.3 + - - +
23O PHE* 2.8 29.3 + - - +
82O ALA* 3.5 6.2 - - - -
83O SER* 2.9 32.7 + - - -
84O VAL* 3.3 23.5 + - + +
109O LEU* 3.9 11.9 - - + +
112O GLU* 3.0 24.4 + - - -
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Residues in contact with LEU 20 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16O GLN* 2.9 26.3 + - + +
19O ASN* 1.3 72.6 - - - +
21O ASN* 1.3 62.2 + - - +
23O PHE* 3.7 4.0 - - + +
24O THR* 3.0 31.0 + - - -
53O PHE* 4.2 24.2 - - + +
56O GLN* 4.2 4.5 - - + +
57O MET* 3.6 44.3 - - + +
60O VAL* 3.8 16.2 - - + -
109O LEU* 4.1 28.0 - - + -
113O TYR* 3.6 26.7 - - + +
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Residues in contact with ASN 21 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M VAL* 4.3 10.7 - - - +
28M HIS* 5.5 0.7 - - - -
32M TRP* 5.2 0.2 - - - -
50M TYR* 5.6 0.7 + - - -
75M LEU* 4.2 3.9 - - + +
17O VAL* 2.6 33.2 + - - +
18O ALA 3.3 3.5 + - - +
19O ASN 3.3 0.2 - - - -
20O LEU* 1.3 76.5 - - - +
22O VAL* 1.3 66.4 + - - +
24O THR* 3.4 11.7 - - - +
25O VAL* 3.4 23.2 + - - +
57O MET* 3.5 37.7 - - - +
78O PHE* 3.6 38.7 - - + -
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Residues in contact with VAL 22 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75M LEU* 4.0 24.7 - - + -
18O ALA 3.2 13.9 + - - +
19O ASN 3.8 6.3 - - - +
21O ASN* 1.3 76.2 - - - +
23O PHE* 1.3 63.5 + - - +
25O VAL* 3.1 6.4 + - - +
26O LYS* 3.1 18.8 + - + +
78O PHE* 4.6 4.5 - - + +
79O LEU* 4.6 9.4 - - + -
82O ALA* 3.8 18.8 - - + -
84O VAL* 3.7 29.8 - - + +
85O GLU 4.5 0.7 - - - +
86O GLU* 4.0 31.5 - - + +
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Residues in contact with PHE 23 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19O ASN 2.8 19.1 + - - +
20O LEU* 3.7 7.6 - - + +
21O ASN 3.2 0.2 - - - -
22O VAL* 1.3 77.2 - - - +
24O THR* 1.3 57.2 + - - +
26O LYS* 3.0 15.2 + - + +
27O ILE* 2.9 44.0 + - + +
30O ILE* 6.2 0.2 - - + -
49O LEU* 4.8 1.6 - - + -
53O PHE* 3.7 43.1 - + + -
84O VAL* 4.5 7.2 - - + -
102O LEU* 3.5 34.3 - - + -
105O THR* 3.6 28.0 - - + -
106O LEU* 4.0 14.1 - - + -
109O LEU* 3.7 22.4 - - + -
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Residues in contact with THR 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M TYR* 5.9 2.7 - - - +
20O LEU 3.0 16.0 + - - +
21O ASN* 3.4 18.8 - - - +
22O VAL 3.3 0.2 - - - -
23O PHE* 1.3 78.7 - - - +
25O VAL* 1.3 70.9 + - + +
27O ILE* 3.2 17.2 + - - +
28O HIS* 3.3 9.4 + - - +
50O TYR* 3.5 53.2 + - + +
53O PHE* 4.3 5.8 - - - +
54O GLY* 4.1 13.8 + - - -
57O MET* 6.3 2.5 - - + -
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Residues in contact with VAL 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M ASN* 4.3 10.1 - - - +
73M SER* 3.5 24.0 - - - +
74M THR* 3.7 7.6 - - - -
75M LEU* 3.4 25.1 - - + -
78M PHE* 3.6 30.7 - - + -
21O ASN 3.7 6.1 - - - +
22O VAL 3.1 8.9 + - - +
24O THR* 1.3 82.1 - - + +
26O LYS* 1.3 62.3 + - - +
28O HIS* 3.2 14.0 + - + +
29O GLN* 3.1 19.1 + - - +
32O TRP* 6.3 0.4 - - + -
86O GLU* 4.6 1.6 - - - +
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Residues in contact with LYS 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73M SER 5.2 1.3 - - - -
22O VAL* 3.1 12.2 + - + +
23O PHE* 3.0 21.9 + - + +
25O VAL* 1.3 75.9 - - - +
27O ILE* 1.3 63.3 + - - +
29O GLN* 2.9 32.8 + - - +
30O ILE* 3.0 25.3 + - + +
84O VAL* 4.4 4.7 - - - -
85O GLU 2.7 31.0 + - - -
86O GLU* 4.1 12.0 - - + +
87O ALA 5.0 1.2 - - - +
101O ASP* 2.6 38.2 + - - +
102O LEU* 5.1 0.2 - - - -
105O THR* 3.4 30.1 - - - +
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Residues in contact with ILE 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O PHE* 2.9 57.0 + - + +
24O THR* 3.2 12.8 + - - +
26O LYS* 1.3 77.1 - - - +
28O HIS* 1.3 61.9 + - - +
30O ILE* 3.4 11.1 + - - +
31O HIS* 3.2 19.3 + - + +
46O MET* 3.2 42.8 - - + +
49O LEU* 3.8 34.3 - - + +
50O TYR* 4.0 12.6 - - + +
53O PHE* 4.4 3.4 - - + -
102O LEU* 5.0 1.8 - - + -
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Residues in contact with HIS 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M ASN* 5.6 1.3 - - - -
54M GLY 5.5 0.2 + - - -
57M MET* 3.8 20.3 - - + +
58M ASP* 3.1 35.1 + - - -
24O THR 3.3 4.7 + - - +
25O VAL* 3.2 14.7 + - + +
26O LYS 3.2 0.6 - - - -
27O ILE* 1.3 76.7 - - - +
29O GLN* 1.3 55.2 + - - +
31O HIS* 3.0 13.4 + + - +
32O TRP* 2.7 67.2 + + + -
47O ASP* 5.8 3.6 + - - -
50O TYR* 3.2 53.6 + + + +
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Residues in contact with GLN 29 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73M SER* 3.1 48.0 + - - +
74M THR* 3.9 0.7 - - - +
25O VAL 3.1 9.9 + - - +
26O LYS* 2.9 28.6 + - - +
28O HIS* 1.3 76.4 - - - +
30O ILE* 1.3 65.3 + - + +
32O TRP* 4.6 1.5 - - - -
33O TYR* 3.1 34.3 + - + +
87O ALA 3.0 28.4 + - - +
89O TYR* 3.9 18.4 + - + +
98O LEU* 5.0 9.6 - - + +
101O ASP* 5.0 5.5 + - - -
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Residues in contact with ILE 30 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O PHE* 6.2 0.2 - - + -
26O LYS* 3.0 31.2 + - + +
27O ILE* 3.8 9.9 - - - +
28O HIS 3.2 0.2 - - - -
29O GLN* 1.3 80.8 - - + +
31O HIS* 1.3 55.5 + - - +
34O MET* 3.0 48.2 + - + +
46O MET* 4.0 7.0 - - - -
98O LEU* 3.5 48.5 - - + +
99O MET* 3.4 26.2 - - + -
101O ASP* 5.2 2.2 - - - +
102O LEU* 3.9 28.0 - - + +
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Residues in contact with HIS 31 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M GLU* 4.1 17.1 + - - -
27O ILE* 3.2 10.5 + - + +
28O HIS* 3.0 17.9 + + - +
30O ILE* 1.3 79.3 - - - +
32O TRP* 1.3 89.3 + + - +
34O MET* 3.2 25.0 - - - +
39O PHE* 4.5 12.4 - + - -
43O GLY* 3.1 40.8 + - - -
46O MET* 3.8 9.4 - - + -
47O ASP* 3.3 20.8 + - - -
144Q TRP* 4.7 11.2 - + - -
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Residues in contact with TRP 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M VAL* 4.6 2.7 - - + -
21M ASN* 5.3 1.3 - - - -
57M MET* 3.7 28.7 - - + -
58M ASP* 4.0 10.5 + - - -
61M ALA* 3.5 24.4 - - + +
62M GLU* 4.7 12.4 + - + +
65M LEU* 3.6 43.2 - - + +
71M PRO* 3.8 18.4 - - + -
72M PHE 3.5 22.7 - - - -
73M SER* 4.1 16.6 - - - -
78M PHE* 5.1 3.8 - + - -
25O VAL* 6.3 0.4 - - + -
28O HIS* 2.7 51.6 + + + +
31O HIS* 1.3 96.0 - + - +
33O TYR* 1.3 71.4 + - + +
34O MET 3.9 1.9 + - - +
39O PHE* 5.7 0.2 - - - -
144Q TRP* 4.4 10.0 + + - -
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Residues in contact with TYR 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65M LEU* 5.1 4.0 - - + -
70M SER* 3.1 25.0 + - - -
71M PRO* 2.7 42.8 + - + -
73M SER* 3.6 22.9 - - - -
29O GLN* 3.1 28.8 + - + +
30O ILE 4.7 0.2 - - - +
32O TRP* 1.3 85.7 - - + +
34O MET* 1.3 66.7 + - - +
35O ARG* 3.5 12.1 + - - +
89O TYR* 3.3 72.0 + + + +
93O LYS 5.2 1.6 - - - +
98O LEU* 4.6 6.3 - - + +
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Residues in contact with MET 34 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O ILE* 3.0 47.0 + - + +
31O HIS* 3.2 16.2 - - - +
32O TRP 3.6 1.8 - - - +
33O TYR* 1.3 79.9 - - - +
35O ARG* 1.3 63.6 + - - +
39O PHE* 3.4 35.6 - - + +
42O LEU* 3.7 14.4 - - + -
43O GLY* 3.6 26.2 - - - -
46O MET* 3.7 18.6 - - + -
95O MET* 3.2 36.1 - - + -
98O LEU* 4.2 7.4 - - + -
99O MET* 4.4 1.3 - - + -
144Q TRP* 5.7 0.3 + - - -
148Q ALA* 4.0 1.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il